Bacterial Community Is Affected by Locations and Time Rather Than Potato Varieties but Streptomyces spp. Are Related to Potato Varieties

Geon Seung Lee,Jae E Yang,Mahesh Adhikari,Duck Hwan Park,Kean-Soo Ha,Hyuck Soo Kim,Kyu Suk Han

doi:10.3390/d13120659

Abstract

Improved knowledge and a better understanding of the functions of bacterial communities are vital for effective crop disease management. This study was conducted to study a bacterial community’s relationship with the common scab in four different potato varieties (Dejima, DJ; Atlantic, DS; Seohong, SH; Haryeong, HY) at two different locations (Gangneung and Chuncheon) and spatial locations (rhizosphere and furrow) at two different times (preharvest and postharvest). In addition, metagenomic sequencing was performed by extracting genomic DNA from soil samples to observe the dominant bacterial microbes and disease severity of the common scab in all the tested varieties in spatial location and time. The results suggest that the most dominant bacterial phyla in all the soil samples were Proteobacteria, Acidobacteria, and Bacteroidetes. Additionally, Streptomyces spp. were found to be more abundant in the susceptible variety (DJ) than in other varieties (DS, SH, and HY). Interestingly, bacterial communities were found to be more diverse across the two different geographical locations, spatial locations, and harvesting times, rather than the variety of potato, according to PCoA analysis. There were no interlinked changes in bacterial communities among the varieties. Moreover, the 14 most dominant bacterial genus correlation networks with Streptomyces spp. suggested that there was a significant positive and negative correlation to some extent. Alpha and beta diversity results clearly indicated that the possible reason for differences in bacterial communities might have been due to the different spatial locations, in comparison with varieties, which suggests that there was no significant correlation between bacterial community richness and diversity among the varieties.

Highlights

The results of this study showed that, in most cases, the bacterial communities were not similar among Gangneung and Chuncheon in postharvest (Figure 1)
Changes in the diversity of bacterial communities were reported for cultivars [40]
In this study the bacterial richness (Chao1), OTUs, and diversity (Shannon) were similar in the DJ, DS, and SH varieties in furrow soil in Gangneung (Supplementary Figure S4); diversity was not similar in furrow soil after harvest. This result suggests that the variations in bacterial communities are due to differences in the soil composition and abundance of root exudates [41]

Summary

Introduction

Microorganisms play a pivotal role in soil environments. Shifts in microbial populations often indicate changes in the soil environment. Soil microorganisms are the most active components of soil decomposition systems [2]. Many researchers have focused on soil microbial communities to improve their application and promote plant health [3]. Soil microbiome analysis via metagenomics sequencing has been introduced to assess the resistivity or susceptibility of plants to diseases [4]. Taking these factors into consideration, soil microbiome structure and functioning can determine plant–pathogen interactions under natural field conditions [5]

Methods

Results

Conclusion